Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment

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Fältnamn	Indikatorer	Metadata
000		12410naa a2201657 4500
001		oai:DiVA.org:liu-200076
003		SwePub
008		240115s2023 \| \|\|\|\|\|\|\|\|\|\|\|000 \|\|eng\|
024	7	a https://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-2000762 URI
024	7	a https://doi.org/10.1002/prot.266092 DOI
040		a (SwePub)liu
041		a engb eng
042		9 SwePub
072	7	a ref2 swepub-contenttype
072	7	a art2 swepub-publicationtype
100	1	a Lensink, Marc F.u Univ Lille, France4 aut
245	1 0	a Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment
264		c 2023
264	1	b WILEY,c 2023
338		a print2 rdacarrier
500		a Funding Agencies\|Francis Crick Institute; Cancer Research UK [FC0001003]; UK Medical Research Council [FC001003]; Wellcome Trust [FC001003]; European Union Horizon 2020 [823830]; Netherlands e-Science Center [027.020.G13]; US National Institutes of Health [R01GM146340, R01GM093123]; Spanish Ministry of Science [501100011033, AEI/10.13039, PID2019-110167RB-I00]; National Institute of Health [R35 GM144083, RM1135136, R35GM118078, R01GM140098, R01GM123055, R01GM133840, R35-GM141881]; Advanced Research Computing at Hopkins (ARCH) core facility; National Natural Science Foundation of China [32161133002, 62072199]; European Molecular Biology Organization (EMBO) [ALTF 145-2021]; Government of Catalonia's Agency for Business Competitiveness (ACCIO); National Science Foundation [DMS 2054251, DBI2003635, IIS2211598, DBI2146026, MCB1925643, CMMI1825941, IIS1763246, DBI1759934, CCF-1943008, OAC1920103]; National Institute of General Medical Sciences [T32 GM132024]; NIH/NIGMS [R35GM136409, R35GM124952]; National Science Center of Poland (Narodowe Centrum Nauki) (NCN) [UMO2017/27/B/ST4/00926, UMO-2017/26/M/ ST4/00044, UMO2017/25/B/ST4/01026]; Research Council of Lithuania [: S-MIP-21-25]; Wallenberg AI, Autonomous System and Software Program (WASP); Knut and Alice Wallenberg Foundation (KAW); Swedish Research Council; Science Foundation of the National Key Laboratory of Science and Technology; Fundamental Research Funds for the Central Universities of China; [801342]
520		a We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average similar to 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem.
650	7	a NATURVETENSKAPx Data- och informationsvetenskapx Bioinformatik0 (SwePub)102032 hsv//swe
650	7	a NATURAL SCIENCESx Computer and Information Sciencesx Bioinformatics0 (SwePub)102032 hsv//eng
653		a AlphaFold; blind prediction; CAPRI; CASP; deep learning; protein assemblies; protein complexes; protein-protein interaction
700	1	a Brysbaert, Guillaumeu Univ Lille, France4 aut
700	1	a Raouraoua, Nessimu Univ Lille, France4 aut
700	1	a Bates, Paul A.u Francis Crick Inst, England4 aut
700	1	a Giulini, Marcou Univ Utrecht, Netherlands4 aut
700	1	a Honorato, Rodrigo V.u Univ Utrecht, Netherlands4 aut
700	1	a van Noort, Charlotteu Univ Utrecht, Netherlands4 aut
700	1	a Teixeira, Joao M. C.u Univ Utrecht, Netherlands4 aut
700	1	a Bonvin, Alexandre M. J. J.u Univ Utrecht, Netherlands4 aut
700	1	a Kong, Renu Jiangsu Univ Technol, Peoples R China4 aut
700	1	a Shi, Hangu Jiangsu Univ Technol, Peoples R China4 aut
700	1	a Lu, Xufengu Jiangsu Univ Technol, Peoples R China4 aut
700	1	a Chang, Shanu Jiangsu Univ Technol, Peoples R China4 aut
700	1	a Liu, Jianu Univ Missouri, MO USA4 aut
700	1	a Guo, Zhiyeu Univ Missouri, MO USA4 aut
700	1	a Chen, Xiaou Univ Missouri, MO USA4 aut
700	1	a Morehead, Alexu Univ Missouri, MO USA4 aut
700	1	a Roy, Raj S.u Univ Missouri, MO USA4 aut
700	1	a Wu, Tianqiu Univ Missouri, MO USA4 aut
700	1	a Giri, Nabinu Univ Missouri, MO USA4 aut
700	1	a Quadir, Farhanu Univ Missouri, MO USA4 aut
700	1	a Chen, Chenu Univ Missouri, MO USA4 aut
700	1	a Cheng, Jianlinu Univ Missouri, MO USA4 aut
700	1	a Del Carpio, Carlos A.u Fukushimuta Hosp, Japan4 aut
700	1	a Ichiishi, Eichirou Int Univ Hlth & Welf IUHV Hosp, Japan4 aut
700	1	a Rodriguez-Lumbreras, Luis A.u CSIC Univ Rioja Gobierno La Rioja, Spain; Barcelona Supercomp Ctr BSC, Spain4 aut
700	1	a Fernandez-Recio, Juanu CSIC Univ Rioja Gobierno La Rioja, Spain; Barcelona Supercomp Ctr BSC, Spain4 aut
700	1	a Harmalkar, Ameyau Johns Hopkins Univ, MD USA4 aut
700	1	a Chu, Lee-Shinu Johns Hopkins Univ, MD USA4 aut
700	1	a Canner, Samu Johns Hopkins Univ, MD USA4 aut
700	1	a Smanta, Rituparnau Johns Hopkins Univ, MD USA4 aut
700	1	a Gray, Jeffrey J.u Johns Hopkins Univ, MD USA; Johns Hopkins Univ, MD USA4 aut
700	1	a Li, Haou Huazhong Univ Sci & Technol, Peoples R China4 aut
700	1	a Lin, Peicongu Huazhong Univ Sci & Technol, Peoples R China4 aut
700	1	a He, Jiahuau Huazhong Univ Sci & Technol, Peoples R China4 aut
700	1	a Tao, Huanyuu Huazhong Univ Sci & Technol, Peoples R China4 aut
700	1	a Huang, Sheng-Youu Huazhong Univ Sci & Technol, Peoples R China4 aut
700	1	a Roel-Touris, Jorgeu Mol Biol Inst Barcelona IBMB CSIC, Spain4 aut
700	1	a Jimenez-Garcia, Brianu Zymvol Biomodeling, Spain4 aut
700	1	a Christoffer, Charles W.u Purdue Univ, IN USA4 aut
700	1	a Jain, Anika J.u Purdue Univ, IN USA4 aut
700	1	a Kagaya, Yukiu Purdue Univ, IN USA4 aut
700	1	a Kannan, Hariniu Purdue Univ, IN USA; Indian Inst Technol Madras, India4 aut
700	1	a Nakamura, Tsukasau Purdue Univ, IN USA4 aut
700	1	a Terashi, Genkiu Purdue Univ, IN USA4 aut
700	1	a Verburgt, Jacob C.u Purdue Univ, IN USA4 aut
700	1	a Zhang, Yuanyuanu Purdue Univ, IN USA4 aut
700	1	a Zhang, Zicongu Purdue Univ, IN USA4 aut
700	1	a Fujuta, Hayatou Indian Inst Technol Madras, India4 aut
700	1	a Sekijima, Masakazuu Tokyo Inst Technol, Japan4 aut
700	1	a Kihara, Daisukeu Purdue Univ, IN USA4 aut
700	1	a Khan, Omeiru Boston Univ, MA USA4 aut
700	1	a Kotelnikov, Sergeiu SUNY Stony Brook, NY USA4 aut
700	1	a Ghani, Usmanu Boston Univ, MA USA4 aut
700	1	a Padhorny, Dzmitryu SUNY Stony Brook, NY USA4 aut
700	1	a Beglov, Dmitriu Boston Univ, MA USA4 aut
700	1	a Vajda, Sandoru Boston Univ, MA USA4 aut
700	1	a Kozakov, Dimau SUNY Stony Brook, NY USA4 aut
700	1	a Negi, Surendra S.u Univ Texas Med Branch, TX USA4 aut
700	1	a Ricciardelli, Tizianau King Abdullah Univ Sci & Technol KAUST, Saudi Arabia4 aut
700	1	a Barradas-Bautista, Didieru King Abdullah Univ Sci & Technol KAUST, Saudi Arabia4 aut
700	1	a Cao, Zhenu King Abdullah Univ Sci & Technol KAUST, Saudi Arabia4 aut
700	1	a Chawla, Mohitu King Abdullah Univ Sci & Technol KAUST, Saudi Arabia4 aut
700	1	a Cavallo, Luigiu King Abdullah Univ Sci & Technol KAUST, Saudi Arabia; Univ Salerno, Italy4 aut
700	1	a Oliva, Rominau Univ Naples Parthenope, Italy4 aut
700	1	a Yin, Ruiu Univ Maryland, MD USA4 aut
700	1	a Cheung, Melyssau Univ Maryland, MD USA; Univ Maryland, MD USA4 aut
700	1	a Guest, Johnathan D.u Univ Maryland, MD USA; Univ Maryland, MD USA4 aut
700	1	a Lee, Jessicau Univ Maryland, MD USA; Univ Maryland, MD USA4 aut
700	1	a Pierce, Brian G.u Univ Maryland, MD USA4 aut
700	1	a Shor, Benu Hebrew Univ Jerusalem, Israel4 aut
700	1	a Cohen, Tomeru Hebrew Univ Jerusalem, Israel4 aut
700	1	a Halfon, Matanu Hebrew Univ Jerusalem, Israel4 aut
700	1	a Schneidman-Duhovny, Dinau Hebrew Univ Jerusalem, Israel4 aut
700	1	a Zhu, Shaowenu Hebrew Univ Jerusalem, Israel; Texas M Univ, TX USA4 aut
700	1	a Yin, Rujieu Texas M Univ, TX USA4 aut
700	1	a Sun, Yuanfeiu Texas M Univ, TX USA4 aut
700	1	a Shen, Yangu Texas M Univ, TX USA; Texas A&M Univ, TX USA; Texas A&M Univ, TX USA; Texas A&M Univ, TX USA4 aut
700	1	a Maszota-Zieleniak, Martynau Univ Gdansk, Poland4 aut
700	1	a Bojarski, Krzysztof K.u Univ Gdansk, Poland; Techn Univ Gdansk, Poland4 aut
700	1	a Lubecka, Emilia A.u Techn Univ Gdansk, Poland4 aut
700	1	a Marcisz, Mateuszu Univ Gdansk, Poland4 aut
700	1	a Danielsson, Annemarieu Univ Gdansk, Poland4 aut
700	1	a Dziadek, Lukaszu Univ Gdansk, Poland4 aut
700	1	a Gaardlos, Margretheu Univ Gdansk, Poland4 aut
700	1	a Gieldon, Arturu Univ Gdansk, Poland4 aut
700	1	a Liwo, Adamu Univ Gdansk, Poland4 aut
700	1	a Samsonov, Sergey A.u Univ Gdansk, Poland4 aut
700	1	a Slusarz, Rafalu Univ Gdansk, Poland4 aut
700	1	a Zieba, Karolinau Univ Gdansk, Poland4 aut
700	1	a Sieradzan, Adam K.u Univ Gdansk, Poland4 aut
700	1	a Czaplewski, Cezaryu Univ Gdansk, Poland4 aut
700	1	a Kobayashi, Shinpeiu Kitasato Univ, Japan4 aut
700	1	a Miyakawa, Yutau Kitasato Univ, Japan4 aut
700	1	a Kiyota, Yasuomiu Kitasato Univ, Japan4 aut
700	1	a Takeda-Shitaka, Mayukou Kitasato Univ, Japan4 aut
700	1	a Olechnovic, Klimentu Vilnius Univ, Lithuania4 aut
700	1	a Valancauskas, Lukasu Vilnius Univ, Lithuania4 aut
700	1	a Dapkunas, Justasu Vilnius Univ, Lithuania4 aut
700	1	a Venclovas, Ceslovasu Vilnius Univ, Lithuania4 aut
700	1	a Wallner, Björn,d 1975-u Linköpings universitet,Bioinformatik,Tekniska fakulteten4 aut0 (Swepub:liu)bjowa51
700	1	a Yang, Linu Harbin Inst Technol, Peoples R China; Univ Sydney, Australia4 aut
700	1	a Hou, Chengyuu Harbin Inst Technol, Peoples R China4 aut
700	1	a He, Xiaodongu Harbin Inst Technol, Peoples R China; Shenzhen STRONG Adv Mat Res Inst Col Ltd, Peoples R China4 aut
700	1	a Guo, Shuaiu Harbin Inst Technol, Peoples R China4 aut
700	1	a Jiang, Shendau Harbin Inst Technol, Peoples R China4 aut
700	1	a Ma, Xiaoliangu Harbin Inst Technol, Peoples R China4 aut
700	1	a Duan, Ruiu Univ Missouri, MO USA4 aut
700	1	a Qui, Limingu Univ Missouri, MO USA4 aut
700	1	a Xu, Xianjinu Univ Missouri, MO USA4 aut
700	1	a Zou, Xiaoqinu Univ Missouri, MO USA; Univ Missouri, MO USA; Univ Missouri, MO USA; Univ Missouri, MO USA4 aut
700	1	a Velankar, Sameeru European Bioinformat Inst EMBL EBI, England4 aut
700	1	a Wodak, Shoshana J.u VUB Ctr Struct Biol VIB, Belgium4 aut
710	2	a Univ Lille, Franceb Francis Crick Inst, England4 org
773	0	t Proteinsd : WILEYx 0887-3585x 1097-0134
856	4 8	u https://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-200076
856	4 8	u https://doi.org/10.1002/prot.26609

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